Contacts of the strand formed by residues 57 - 63 (chain D) in PDB entry 2GJD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLY 4.5 9.9 - - - +
25D TYR* 3.8 31.5 + - + +
44D GLY* 4.1 11.0 - - - -
45D ILE 3.5 7.9 - - - +
46D PRO* 4.4 11.7 - - + -
55D GLY 4.7 2.2 - - - +
56D GLY* 1.3 74.6 - - - +
58D TYR* 1.3 63.0 + - - +
59D PRO* 3.6 5.7 - - - +
155D TYR* 2.9 26.5 + - - +
157D LYS* 4.0 32.8 - - + -
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Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLY* 3.5 1.7 - - - -
45D ILE* 2.8 57.3 + - + +
47D GLY* 3.7 9.0 - - - -
53D TRP* 2.6 51.6 + + - -
56D GLY* 3.6 17.6 - - - -
57D VAL* 1.3 71.4 - - - +
59D PRO* 1.3 69.6 - - + +
60D ILE* 3.7 1.0 + - - +
77D PHE* 3.7 22.0 - - + -
81D PHE* 3.6 22.7 - + + -
120D LEU* 3.9 15.0 - - + -
151D GLN* 4.0 13.2 - - + -
152D ALA* 3.3 18.7 - - - +
155D TYR* 3.6 28.3 - + + -
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Residues in contact with PRO 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR* 4.3 10.8 - - - +
43D ALA 3.4 9.4 - - - +
44D GLY* 4.4 1.6 - - - -
57D VAL 3.6 3.6 - - - +
58D TYR* 1.3 84.7 - - + +
60D ILE* 1.3 60.3 + - - +
77D PHE* 3.5 7.8 - - - -
78D PRO* 3.3 36.2 - - + +
155D TYR* 3.4 37.2 - - + -
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLU* 3.5 4.9 - - - +
43D ALA* 2.8 59.2 + - + +
45D ILE* 4.0 24.0 - - + -
58D TYR 3.7 2.7 + - - +
59D PRO* 1.3 72.5 - - - +
61D THR* 1.3 64.8 + - - +
62D VAL* 4.1 10.1 - - + -
75D VAL* 3.6 27.1 - - + -
76D LYS 3.1 12.1 - - - +
77D PHE* 3.5 38.8 - - + -
92D ILE* 4.4 1.3 - - + -
112D ILE* 5.9 1.1 - - + -
113D VAL* 4.4 8.7 - - + -
116D VAL* 5.1 4.3 - - + -
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LYS* 4.6 21.1 - - - +
41D TRP 3.3 8.3 - - - +
42D GLU* 4.4 15.0 - - + +
60D ILE* 1.3 77.2 - - - +
62D VAL* 1.3 66.0 + - - +
63D GLU* 4.1 7.3 - - - -
74D LYS 3.6 1.3 - - - +
75D VAL* 3.4 5.9 - - - +
76D LYS* 2.9 52.4 + - - +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN 3.8 0.7 - - - +
40D LYS* 3.3 5.9 - - - +
41D TRP* 2.9 43.7 + - + +
43D ALA* 4.7 5.8 - - + -
60D ILE* 4.1 24.7 - - + -
61D THR* 1.3 77.9 - - - +
63D GLU* 1.3 62.9 - - - +
64D TYR* 3.6 37.0 + - + +
73D PRO* 3.7 19.1 - - + -
74D LYS 3.5 1.8 - - - -
75D VAL* 4.2 11.7 - - + -
109D LEU* 4.5 16.6 - - + -
112D ILE* 6.0 0.2 - - + -
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LYS* 5.6 3.3 + - - -
39D GLN 3.6 5.4 - - - +
40D LYS* 4.3 27.9 + - + +
61D THR* 4.8 7.0 - - - +
62D VAL* 1.3 79.1 - - - +
64D TYR* 1.3 63.6 + - - +
65D PRO* 3.5 2.8 - - - +
73D PRO* 3.3 2.4 - - - +
74D LYS* 2.8 67.8 + - + +
76D LYS* 3.7 20.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il